There are several other functions that only some users may need that are not exported by default. Everyone may need a different subset of those, so I think leaving it up to the user to specify them is still a good solution. Maybe it should be documented better, but as you noticed yourself the list of potentially useful stuff also keeps changing with every Emscripten release, so it's difficult to provide a list of options.
Here's what I use on a custom libopenmpt.js build that requires all sorts of metadata extraction, before invoking make:
export CXXFLAGS="-s \"EXTRA_EXPORTED_RUNTIME_METHODS=['lengthBytesUTF8','stackAlloc','stackSave','stackRestore','stringToUTF8','Pointer_stringify','writeArrayToMemory']\""